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Zhao B, Liu C, Qi Y, Zhang T, Wang Y, He X, Wang L, Jin T. Preliminary study of identified novel susceptibility loci for HAPE risk in a Chinese male Han population. Per Med 2024:1-15. [PMID: 38940394 DOI: 10.1080/17410541.2024.2365617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 06/05/2024] [Indexed: 06/29/2024]
Abstract
High altitude pulmonary edema (HAPE) is a life-threatening form of non-cardiogenic pulmonary edema. In recent years, association studies have become the main method for identifying HAPE genetic loci. A genome-wide association study (GWAS) of HAPE risk-associated loci was performed in Chinese male Han individuals (164 HAPE cases and 189 healthy controls) by the Precision Medicine Diversity Array Chip with 2,771,835 loci (Applied Biosystems Axiom™). Eight overlapping candidate loci in CCNG2, RP11-445O3.2, NUPL1 and WWOX were finally selected. In silico functional analyses displayed the PPI network, functional enrichment and signal pathways related to CCNG2, NUPL1, WWOX and NRXN1. This study provides data supplements for HAPE susceptibility gene loci and new insights into HAPE susceptibility.
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Affiliation(s)
- Beibei Zhao
- School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China
| | - Changchun Liu
- School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China
| | - Yijin Qi
- School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China
| | - Tianyi Zhang
- School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China
| | - Yuhe Wang
- Department of Clinical Laboratory, The Affiliated Hospital of Xizang Minzu University, Xianyang, Shaanxi 712082, China
| | - Xue He
- School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China
| | - Li Wang
- School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China
| | - Tianbo Jin
- School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China
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Lin Z, Zhang J, Chen Q, Zhang X, Zhang D, Lin J, Lin D. Transcriptome analysis of the adenoma-carcinoma sequences identifies novel biomarkers associated with development of canine colorectal cancer. Front Vet Sci 2023; 10:1192525. [PMID: 38098990 PMCID: PMC10720982 DOI: 10.3389/fvets.2023.1192525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 10/11/2023] [Indexed: 12/17/2023] Open
Abstract
The concept of adenoma-to-cancer transformation in human colorectal cancer (CRC) is widely accepted. However, the relationship between transcriptome features and adenoma to carcinoma transformation in canines is not clear. We collected transcriptome data from 8 normal colon tissues, 4 adenoma tissues, and 15 cancer tissues. Differential analysis was unable to determine the dynamic changes of genes but revealed that PFKFB3 may play a key role in this process. Enrichment analysis explained metabolic dysregulation, immunosuppression, and typical cancer pathways in canine colorectal tumors. MFuzz generated specific dynamic expression patterns of five differentially expressed genes (DEGs). Weighted correlation network analysis showed that DEGs in cluster 3 were associated with malignant tissues, revealing the key role of inflammatory and immune pathways in canine CRC, and the S100A protein family was also found to be involved in the malignant transformation of canine colorectal tumors. By comparing strategies between humans and dogs, we found five novel markers that may be drivers of CRC. Among them, GTBP4 showed excellent diagnostic and prognostic ability. This study was the first systematic exploration of transformation in canine CRC, complemented the molecular characteristics of the development and progression of canine CRC, and provided new potential biomarkers and comparative oncologic evidence for biomarker studies in human colorectal cancer.
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Affiliation(s)
- Zixiang Lin
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Jiatong Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Qi Chen
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiaohu Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Di Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jiahao Lin
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Degui Lin
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
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Méric T, Issard J, Maufras T, Hugonnard M, Senecat O, Lecoindre A, Leal RO, Bertolani C, Toulza O, Lecoindre P, Brisebard E, Ledevin M, Larcher T, Drut A, Darnis E, Hernandez J. Recurrence and survival in dogs with excised colorectal polyps: A retrospective study of 58 cases. J Vet Intern Med 2023; 37:2375-2384. [PMID: 37772917 PMCID: PMC10658478 DOI: 10.1111/jvim.16876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 09/11/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND Compared to humans, colorectal polyps are relatively rare in dogs. Epidemiological and prognostic data remain accordingly sparse, although they could help veterinary clinicians in the management of these cases. OBJECTIVES To report the epidemiological data of dogs with colorectal polyps and identify factors associated with recurrence and survival. ANIMALS Fifty-eight client-owned dogs with colorectal polyps admitted to 7 veterinary hospitals (53 dogs from France, 5 dogs from Spain, and 4 dogs from Portugal) were included. METHODS Retrospective multicentric cohort study. Medical records and long-term outcome of the dogs were reviewed. When available, histological samples were reassessed by 2 board-certified pathologists according to the revised Vienna classification (RVC). RESULTS The West Highland White Terrier (WHWT) breed was significantly associated with the presence of colorectal polyps (OR: 20; 95% CI: 7.5-52; P < .001). The overall median time to recurrence was not reached after 2000 days. The overall estimated median survival time was 1640 days. WHWT breed and larger polyps were significantly associated with a shorter time of polyp recurrence after surgical removal (respectively, P = .05 and P = .01). CONCLUSIONS AND CLINICAL IMPORTANCE The probability of recurrence of colorectal polyps in dogs is low, but increased in WHWTs and larger polyps, which might benefit from routine screening after removal. No effective predictors of polyp recurrence and survival were identified using the RVC.
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Affiliation(s)
- Tristan Méric
- Oniris VetAgroBio Nantes, Université de NantesNantesFrance
| | - Julien Issard
- Oniris VetAgroBio Nantes, Université de NantesNantesFrance
| | | | - Marine Hugonnard
- Centre Hospitalier Universitaire Vétérinaire VetAgro SupUniversité de LyonFrance
| | - Odile Senecat
- Oniris VetAgroBio Nantes, Université de NantesNantesFrance
| | | | - Rodolfo Oliveira Leal
- CIISA—Centre for Interdisciplinary Research in Animal Health/Faculty of Veterinary MedicineUniversity of Lisbon; Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalSLisbonPortugal
| | | | | | | | | | | | | | - Amandine Drut
- Oniris VetAgroBio Nantes, Université de NantesNantesFrance
| | | | - Juan Hernandez
- Oniris VetAgroBio Nantes, Université de NantesNantesFrance
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Watson J, Wang T, Ho KL, Feng Y, Mahawan T, Dobbin KK, Zhao S. Human basal-like breast cancer is represented by one of the two mammary tumor subtypes in dogs. Breast Cancer Res 2023; 25:114. [PMID: 37789381 PMCID: PMC10546663 DOI: 10.1186/s13058-023-01705-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/31/2023] [Indexed: 10/05/2023] Open
Abstract
BACKGROUND About 20% of breast cancers in humans are basal-like, a subtype that is often triple-negative and difficult to treat. An effective translational model for basal-like breast cancer is currently lacking and urgently needed. To determine whether spontaneous mammary tumors in pet dogs could meet this need, we subtyped canine mammary tumors and evaluated the dog-human molecular homology at the subtype level. METHODS We subtyped 236 canine mammary tumors from 3 studies by applying various subtyping strategies on their RNA-seq data. We then performed PAM50 classification with canine tumors alone, as well as with canine tumors combined with human breast tumors. We identified feature genes for human BLBC and luminal A subtypes via machine learning and used these genes to repeat canine-alone and cross-species tumor classifications. We investigated differential gene expression, signature gene set enrichment, expression association, mutational landscape, and other features for dog-human subtype comparison. RESULTS Our independent genome-wide subtyping consistently identified two molecularly distinct subtypes among the canine tumors. One subtype is mostly basal-like and clusters with human BLBC in cross-species PAM50 and feature gene classifications, while the other subtype does not cluster with any human breast cancer subtype. Furthermore, the canine basal-like subtype recaptures key molecular features (e.g., cell cycle gene upregulation, TP53 mutation) and gene expression patterns that characterize human BLBC. It is enriched in histological subtypes that match human breast cancer, unlike the other canine subtype. However, about 33% of canine basal-like tumors are estrogen receptor negative (ER-) and progesterone receptor positive (PR+), which is rare in human breast cancer. Further analysis reveals that these ER-PR+ canine tumors harbor additional basal-like features, including upregulation of genes of interferon-γ response and of the Wnt-pluripotency pathway. Interestingly, we observed an association of PGR expression with gene silencing in all canine tumors and with the expression of T cell exhaustion markers (e.g., PDCD1) in ER-PR+ canine tumors. CONCLUSIONS We identify a canine mammary tumor subtype that molecularly resembles human BLBC overall and thus could serve as a vital translational model of this devastating breast cancer subtype. Our study also sheds light on the dog-human difference in the mammary tumor histology and the hormonal cycle.
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Affiliation(s)
- Joshua Watson
- Institute of Bioinformatics, University of Georgia, 120 E Green Street, Athens, GA, 30602, USA
| | - Tianfang Wang
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, 120 E Green Street, Athens, GA, 30602, USA
| | - Kun-Lin Ho
- Institute of Bioinformatics, University of Georgia, 120 E Green Street, Athens, GA, 30602, USA
| | - Yuan Feng
- Institute of Bioinformatics, University of Georgia, 120 E Green Street, Athens, GA, 30602, USA
| | - Tanakamol Mahawan
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Kevin K Dobbin
- Department of Biostatistics, University of Georgia, Athens, GA, 30602, USA
| | - Shaying Zhao
- Institute of Bioinformatics, University of Georgia, 120 E Green Street, Athens, GA, 30602, USA.
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, 120 E Green Street, Athens, GA, 30602, USA.
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Lin Z, Chen Q, Zhou J, Zhang J, Zhang X, Zhang D, Lin J, Lin D. Transcriptomic analysis reveals immune infiltration status and potential biomarkers of canine colorectal cancer. Vet Immunol Immunopathol 2023; 262:110622. [PMID: 37478614 DOI: 10.1016/j.vetimm.2023.110622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/30/2023] [Accepted: 06/12/2023] [Indexed: 07/23/2023]
Abstract
Colorectal cancer (CRC) in dogs has been shown to have similar molecular characteristics to human colorectal cancer. Although researchers have explored the pathogenesis and immune status of human CRC, the canine CRC has been far less studied. As a result, we analyzed canine colorectal tumors and normal canine intestinal samples by Gene Set Enrichment Analysis (GSEA) and found significant enrichment of immune-related pathways, including the TNF-α signaling pathway and IL6-STAT3 signaling pathway. In addition, the differential infiltration of naive B cells and regulatory T cells suggested that canine CRC was in a state of immunosuppression. Weighted gene co-expression network analysis (WGCNA) revealed the gene modules that contribute to differences in regulatory T cell inetfiltration, Further cross-validation of canine and human CRC differential genes obtained three core genes that are both species-conserved and differentially expressed, CD44, NAT10, and ETV4, of which NAT10 and ETV4 have been little studied in the immune status of colorectal cancer. Our findings may have implications for the pathogenesis and progression of CRC in dogs and could be a new potential therapeutic target for CMT and provide a bioinformatics foundation for later clinical experiment validation.
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Affiliation(s)
- Zixiang Lin
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Qi Chen
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Jiajing Zhou
- Department of Oncology, Yantai Hospital of Traditional Chinese Medicine, Yantai 264000, Shandong, China
| | - Jiatong Zhang
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Xiaohu Zhang
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Di Zhang
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
| | - Jiahao Lin
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; Department of Center of Research and Innovation of Traditional Chinese Veterinary Medicine, China Agri-cultural University, Beijing 100193, China.
| | - Degui Lin
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
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Rodrigues L, Watson J, Feng Y, Lewis B, Harvey G, Post G, Megquier K, White ME, Lambert L, Miller A, Lopes C, Zhao S. Shared hotspot mutations in oncogenes position dogs as an unparalleled comparative model for precision therapeutics. Sci Rep 2023; 13:10935. [PMID: 37414794 PMCID: PMC10325973 DOI: 10.1038/s41598-023-37505-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/22/2023] [Indexed: 07/08/2023] Open
Abstract
Naturally occurring canine cancers have remarkable similarities to their human counterparts. To better understand these similarities, we investigated 671 client-owned dogs from 96 breeds with 23 common tumor types, including those whose mutation profile are unknown (anal sac carcinoma and neuroendocrine carcinoma) or understudied (thyroid carcinoma, soft tissue sarcoma and hepatocellular carcinoma). We discovered mutations in 50 well-established oncogenes and tumor suppressors, and compared them to those reported in human cancers. As in human cancer, TP53 is the most commonly mutated gene, detected in 22.5% of canine tumors overall. Canine tumors share mutational hotspots with human tumors in oncogenes including PIK3CA, KRAS, NRAS, BRAF, KIT and EGFR. Hotspot mutations with significant association to tumor type include NRAS G61R and PIK3CA H1047R in hemangiosarcoma, ERBB2 V659E in pulmonary carcinoma, and BRAF V588E (equivalent of V600E in humans) in urothelial carcinoma. Our findings better position canines as a translational model of human cancer to investigate a wide spectrum of targeted therapies.
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Affiliation(s)
- Lucas Rodrigues
- One Health Company, Inc, 530 Lytton Ave, 2nd Floor, Palo Alto, CA, 94301, USA.
| | - Joshua Watson
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, B304B Life Sciences Building, 120 Green Street, Athens, GA, 30602-7229, USA
| | - Yuan Feng
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, B304B Life Sciences Building, 120 Green Street, Athens, GA, 30602-7229, USA
| | - Benjamin Lewis
- One Health Company, Inc, 530 Lytton Ave, 2nd Floor, Palo Alto, CA, 94301, USA
| | - Garrett Harvey
- One Health Company, Inc, 530 Lytton Ave, 2nd Floor, Palo Alto, CA, 94301, USA
| | - Gerald Post
- One Health Company, Inc, 530 Lytton Ave, 2nd Floor, Palo Alto, CA, 94301, USA
| | - Kate Megquier
- One Health Company, Inc, 530 Lytton Ave, 2nd Floor, Palo Alto, CA, 94301, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Michelle E White
- One Health Company, Inc, 530 Lytton Ave, 2nd Floor, Palo Alto, CA, 94301, USA
| | - Lindsay Lambert
- One Health Company, Inc, 530 Lytton Ave, 2nd Floor, Palo Alto, CA, 94301, USA
| | - Aubrey Miller
- One Health Company, Inc, 530 Lytton Ave, 2nd Floor, Palo Alto, CA, 94301, USA
| | - Christina Lopes
- One Health Company, Inc, 530 Lytton Ave, 2nd Floor, Palo Alto, CA, 94301, USA
| | - Shaying Zhao
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, B304B Life Sciences Building, 120 Green Street, Athens, GA, 30602-7229, USA.
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Feng Y, Hess PR, Tompkins SM, Hildebrand WH, Zhao S. A Kmer-based paired-end read de novo assembler and genotyper for canine MHC class I genotyping. iScience 2023; 26:105996. [PMID: 36798440 PMCID: PMC9926114 DOI: 10.1016/j.isci.2023.105996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/28/2022] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
The major histocompatibility complex class I (MHC-I) genes are highly polymorphic. MHC-I genotyping is required for determining the peptide epitopes available to an individual's T-cell repertoire. Current genotyping software tools do not work for the dog, due to very limited known canine alleles. To address this, we developed a Kmer-based paired-end read (KPR) de novo assembler and genotyper, which assemble paired-end RNA-seq reads from MHC-I regions into contigs, and then genotype each contig and estimate its expression level. KPR tools outperform other popular software examined in typing new alleles. We used KPR tools to successfully genotype152 dogs from a published dataset. The study discovers 33 putative new alleles, finds dominant alleles in 4 dog breeds, and builds allele diversity and expression landscapes among the 152 dogs. Our software meets a significant need in biomedical research.
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Affiliation(s)
- Yuan Feng
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Paul R. Hess
- Department of Clinical Sciences, North Carolina State University, College of Veterinary Medicine, Raleigh, NC 27607, USA
| | - Stephen M. Tompkins
- Center for Vaccines and Immunology, University of Georgia, UGA, Athens, GA 30602, USA
| | - William H. Hildebrand
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Shaying Zhao
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA,Corresponding author
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Li K, Yang J, Zhou X, Wang H, Ren Y, Huang Y, Liu H, Zhong Z, Peng G, Zheng C, Zhou Z. The Mechanism of Important Components in Canine Fecal Microbiota Transplantation. Vet Sci 2022; 9:vetsci9120695. [PMID: 36548856 PMCID: PMC9786814 DOI: 10.3390/vetsci9120695] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Fecal microbiota transplantation (FMT) is a potential treatment for many intestinal diseases. In dogs, FMT has been shown to have positive regulation effects in treating Clostridioides difficile infection (CDI), inflammatory bowel disease (IBD), canine parvovirus (CPV) enteritis, acute diarrhea (AD), and acute hemorrhagic diarrhea syndrome (AHDS). FMT involves transplanting the functional components of a donor's feces into the gastrointestinal tract of the recipient. The effective components of FMT not only include commensal bacteria, but also include viruses, fungi, bacterial metabolites, and immunoglobulin A (IgA) from the donor feces. By affecting microbiota and regulating host immunity, these components can help the recipient to restore their microbial community, improve their intestinal barrier, and induce anti-inflammation in their intestines, thereby affecting the development of diseases. In addition to the above components, mucin proteins and intestinal epithelial cells (IECs) may be functional ingredients in FMT as well. In addition to the abovementioned indications, FMT is also thought to be useful in treating some other diseases in dogs. Consequently, when preparing FMT fecal material, it is important to preserve the functional components involved. Meanwhile, appropriate fecal material delivery methods should be chosen according to the mechanisms these components act by in FMT.
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Affiliation(s)
- Kerong Li
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
- Chengdu Center for Animal Disease Prevention and Control, Chengdu 610041, China
| | - Jie Yang
- Sichuan Institute of Musk Deer Breeding, Chengdu 610016, China
| | - Xiaoxiao Zhou
- Chengdu Center for Animal Disease Prevention and Control, Chengdu 610041, China
| | - Huan Wang
- Sichuan Institute of Musk Deer Breeding, Chengdu 610016, China
| | - Yuxin Ren
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
- Chengdu Center for Animal Disease Prevention and Control, Chengdu 610041, China
| | - Yunchuan Huang
- Chengdu Center for Animal Disease Prevention and Control, Chengdu 610041, China
| | - Haifeng Liu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhijun Zhong
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Guangneng Peng
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Chengli Zheng
- Sichuan Institute of Musk Deer Breeding, Chengdu 610016, China
- Correspondence: (C.Z.); (Z.Z.)
| | - Ziyao Zhou
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (C.Z.); (Z.Z.)
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Móz LES, Martins RHG, Lapa RML, Villacis RAR, Dos Reis PP, Rogatto SR. DNA rare copy number alterations in Reinke’s Edema. Braz J Otorhinolaryngol 2022; 89:279-284. [PMID: 36243603 PMCID: PMC10071534 DOI: 10.1016/j.bjorl.2022.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/21/2022] [Accepted: 09/08/2022] [Indexed: 11/29/2022] Open
Abstract
INTRODUCTION Reinke's Edema (RE) is a laryngeal lesion related to excessive tobacco smoking, voice overuse, and laryngopharyngeal reflux. Although the risk of malignancy has been considered low in literature, RE is classified among precancerous lesions. OBJECTIVES We investigated DNA Copy Number Alterations (CNAs) in specimens of RE and its potential association with malignant progression. METHODS We used array-based comparative genomic hybridization (aCGH, Agilent 4 × 180 K platform) to study eight RE cases. All patients were heavy tobacco users for at least 30 years, and none of them progressed to cancer in the follow-up (>8 years). Two RE presented mild dysplasia, one moderate dysplasia, and no histological alterations were found in the remaining five cases. CNAs were compared with the Database of Genomic Variants (DGV) and genes mapped on altered regions had their functions annotated. RESULTS Six of eight patients showed different rare copy number alterations on chromosomes 2q37.3, 4q13.1, 4q13.3, 7q11.22, 10p14, and 13q34. A gain of the whole chromosome 8 were detected in one case. Of interest, four of eight RE cases showed copy number imbalances involving genes previously described in several tumor types (RASA3, COL6A3, LINC00707, LINP1, SMR3A, and SMR3B). CONCLUSION The genomic imbalances herein found in RE have the potential to contribute to the phenotype but with limited or no risk of cancer. A long-term follow-up in a large series of patients could clarify the mechanisms involved in the malignant progression of RE. LEVEL OF EVIDENCE: 4
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Affiliation(s)
- Luis Eduardo Silva Móz
- Faculdade de Ciências Médicas da Santa Casa de São Paulo, São Paulo, SP, Brazil; São Camilo Oncologia
| | - Regina Helena Garcia Martins
- Universidade Estadual Paulista (UNESP), Faculdade de Medicina, Departamento de Especialidades Cirúrgicas e Anestesiologia, Botucatu, SP, Brazil.
| | - Rainer Marco Lopez Lapa
- National University Toribio Rodríguez de Mendoza of Amazonas, Institute of Livestock and Biotechnology, Laboratory of Molecular Physiology, Chachapoyas, Peru
| | - Rolando André Rios Villacis
- Universidade de Brasília (UnB), Instituto de Ciências Biológicas, Departamento de Genética e Morfologia, Brasília, DF, Brazil
| | - Patricia Pintor Dos Reis
- Universidade Estadual Paulista (UNESP), Faculdade de Medicina, Departamento de Cirurgia e Ortopedia, Botucatu, SP, Brazil
| | - Silvia Regina Rogatto
- University Hospital of Southern Denmark, Department of Clinical Genetics, Vejle, Denmark; University of Southern Denmark, Institute of Regional Health Research, Odense, Denmark.
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10
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Wu Q, Chen JD, Zhou Z. AVL9 promotes colorectal carcinoma cell migration via regulating EGFR expression. Biol Proced Online 2022; 24:1. [PMID: 34991461 PMCID: PMC8903581 DOI: 10.1186/s12575-021-00162-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 12/08/2021] [Indexed: 12/24/2022] Open
Abstract
Background Despite advanced treatments could inhibit progression of colorectal carcinoma (CRC), the recurrence and metastasis remain challenging issues. Accumulating evidences implicated that AVL9 played a vital role in human cancers, but it’s biological function and mechanism in CRC remain unclear. Aim To investigate the biological role and mechanism of AVL9 in colorectal carcinoma. Results AVL9 expression was significantly upregulated in tumor tissues than that in matched normal tissues both at mRNA and protein levels. High expression of AVL9 was closely correlated with M status, stages and poor prognosis of colorectal carcinoma (CRC) patients. Functionally, AVL9 overexpression promoted cell migration rather than cell proliferation in vitro, whereas AVL9 knockdown exhibited the contrary results. Mechanistically, AVL9 regulated EGFR expression, and knockdown of EGFR restrained AVL9-induced cell migration. Conclusion These findings demonstrated that AVL9 contributed to CRC cell migration by regulating EGFR expression, suggesting a potential biomarker and treatment target for CRC.
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Affiliation(s)
- Qiong Wu
- Department of Oncology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Jing De Chen
- Department of Oncology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China.
| | - Zhuqing Zhou
- Department of Gastrointestinal Surgery, School of Medicine, Tongji University, Shanghai, 200120, China.
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11
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Zhong H, Wang J, Zhu Y, Shen Y. Comprehensive Analysis of a Nine-Gene Signature Related to Tumor Microenvironment in Lung Adenocarcinoma. Front Cell Dev Biol 2021; 9:700607. [PMID: 34540825 PMCID: PMC8440811 DOI: 10.3389/fcell.2021.700607] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/04/2021] [Indexed: 01/29/2023] Open
Abstract
Lung adenocarcinoma (LUAD) is the most common malignancy, leading to more than 1 million related deaths each year. Due to low long-term survival rates, the exploration of molecular mechanisms underlying LUAD progression and novel prognostic predictors is urgently needed to improve LUAD treatment. In our study, cancer-specific differentially expressed genes (DEGs) were identified using the robust rank aggregation (RRA) method between tumor and normal tissues from six Gene Expression Omnibus databases (GSE43458, GSE62949, GSE68465, GSE115002, GSE116959, and GSE118370), followed by a selection of prognostic modules using weighted gene co-expression network analysis. Univariate Cox regression, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression analyses were applied to identify nine hub genes (CBFA2T3, CR2, SEL1L3, TM6SF1, TSPAN32, ITGA6, MAPK11, RASA3, and TLR6) that constructed a prognostic risk model. The RNA expressions of nine hub genes were validated in tumor and normal tissues by RNA-sequencing and single-cell RNA-sequencing, while immunohistochemistry staining from the Human Protein Atlas database showed consistent results in the protein levels. The risk model revealed that high-risk patients were associated with poor prognoses, including advanced stages and low survival rates. Furthermore, a multivariate Cox regression analysis suggested that the prognostic risk model could be an independent prognostic factor for LUAD patients. A nomogram that incorporated the signature and clinical features was additionally built for prognostic prediction. Moreover, the levels of hub genes were related to immune cell infiltration in LUAD microenvironments. A CMap analysis identified 13 small molecule drugs as potential agents based on the risk model for LUAD treatment. Thus, we identified a prognostic risk model including CBFA2T3, CR2, SEL1L3, TM6SF1, TSPAN32, ITGA6, MAPK11, RASA3, and TLR6 as novel biomarkers and validated their prognostic and predicted values for LUAD.
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Affiliation(s)
- Haihui Zhong
- Department of Thoracic Surgery, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou Academy of Medical Sciences, Meizhou, China
| | - Jie Wang
- Institute for Pathology, University Hospital of Cologne, Cologne, Germany
| | - Yaru Zhu
- Department of Critical Care Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yefeng Shen
- Institute for Pathology, University Hospital of Cologne, Cologne, Germany
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12
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Jung H, Bae K, Lee JY, Kim JH, Han HJ, Yoon HY, Yoon KA. Establishment of Canine Transitional Cell Carcinoma Cell Lines Harboring BRAF V595E Mutation as a Therapeutic Target. Int J Mol Sci 2021; 22:ijms22179151. [PMID: 34502061 PMCID: PMC8430554 DOI: 10.3390/ijms22179151] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/20/2021] [Accepted: 08/20/2021] [Indexed: 12/22/2022] Open
Abstract
Transitional cell carcinoma (TCC) is the most common malignant tumor of the canine urinary tract and tends to have a poor prognosis due to its invasive potential. Recent studies have reported that up to 80% of canine urothelial carcinoma has the BRAF V595E mutation, which is homologous to the human V600E mutation. Activating the BRAF mutation is an actionable target for developing effective therapeutic agents inhibiting the BRAF/mitogen-activated protein kinase (MAPK) pathway in canine cancer as well as human cancer. We established novel canine TCC cell lines from two tumor tissues and one metastatic lymph node of canine TCC patients harboring the BRAF V595E mutation. Tumor tissues highly expressed the BRAF mutant and phosphorylated extracellular signal-related kinases (ERK)1/2 proteins. The derived cell lines demonstrated activated MAPK pathways. We also evaluated the cell lines for sensitivity to BRAF inhibitors. Sorafenib, a multiple kinase inhibitor targeting RAF/vascular endothelial growth factor receptor (VEGFR), successfully inhibited the BRAF/MAPK pathway and induced apoptosis. The established canine TCC cell lines responded with greater sensitivity to sorafenib than to vemurafenib, which is known as a specific BRAF inhibitor in human cancer. Our results demonstrated that canine TCC cells showed different responses compared to human cancer with the BRAF V600E mutation. These cell lines would be valuable research materials to develop therapeutic strategies for canine TCC patients.
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Affiliation(s)
- Hyojik Jung
- Department of Veterinary Biochemistry, College of Veterinary Medicine, Konkuk University, Seoul 05029, Korea; (H.J.); (K.B.); (J.Y.L.)
| | - Kieun Bae
- Department of Veterinary Biochemistry, College of Veterinary Medicine, Konkuk University, Seoul 05029, Korea; (H.J.); (K.B.); (J.Y.L.)
| | - Ja Young Lee
- Department of Veterinary Biochemistry, College of Veterinary Medicine, Konkuk University, Seoul 05029, Korea; (H.J.); (K.B.); (J.Y.L.)
| | - Jung-Hyun Kim
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, Konkuk University, Seoul 05029, Korea;
| | - Hyun-Jung Han
- Department of Veterinary Emergency and Critical Care, College of Veterinary Medicine, Konkuk University, Seoul 05029, Korea;
| | - Hun-Young Yoon
- Department of Veterinary Surgery, College of Veterinary Medicine, Konkuk University, Seoul 05029, Korea;
| | - Kyong-Ah Yoon
- Department of Veterinary Biochemistry, College of Veterinary Medicine, Konkuk University, Seoul 05029, Korea; (H.J.); (K.B.); (J.Y.L.)
- Correspondence: ; Tel.: +82-2-450-3789; Fax: +82-2-450-3037
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13
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Alsaihati BA, Ho KL, Watson J, Feng Y, Wang T, Dobbin KK, Zhao S. Canine tumor mutational burden is correlated with TP53 mutation across tumor types and breeds. Nat Commun 2021; 12:4670. [PMID: 34344882 PMCID: PMC8333103 DOI: 10.1038/s41467-021-24836-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 07/08/2021] [Indexed: 02/07/2023] Open
Abstract
Spontaneous canine cancers are valuable but relatively understudied and underutilized models. To enhance their usage, we reanalyze whole exome and genome sequencing data published for 684 cases of >7 common tumor types and >35 breeds, with rigorous quality control and breed validation. Our results indicate that canine tumor alteration landscape is tumor type-dependent, but likely breed-independent. Each tumor type harbors major pathway alterations also found in its human counterpart (e.g., PI3K in mammary tumor and p53 in osteosarcoma). Mammary tumor and glioma have lower tumor mutational burden (TMB) (median < 0.5 mutations per Mb), whereas oral melanoma, osteosarcoma and hemangiosarcoma have higher TMB (median ≥ 1 mutations per Mb). Across tumor types and breeds, TMB is associated with mutation of TP53 but not PIK3CA, the most mutated genes. Golden Retrievers harbor a TMB-associated and osteosarcoma-enriched mutation signature. Here, we provide a snapshot of canine mutations across major tumor types and breeds.
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Affiliation(s)
- Burair A Alsaihati
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA, USA
- National Center for Genomics Technology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Kun-Lin Ho
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Joshua Watson
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Yuan Feng
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Tianfang Wang
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Kevin K Dobbin
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, GA, USA
| | - Shaying Zhao
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA, USA.
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14
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Wei D, Sun L, Feng W. hsa_circ_0058357 acts as a ceRNA to promote non‑small cell lung cancer progression via the hsa‑miR‑24‑3p/AVL9 axis. Mol Med Rep 2021; 23:470. [PMID: 33880595 PMCID: PMC8097761 DOI: 10.3892/mmr.2021.12109] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 03/11/2021] [Indexed: 12/20/2022] Open
Abstract
Abnormal circular RNAs (circRNAs) are associated with biological processes in cancer; however, the function of circRNAs remains largely unknown in non-small cell lung cancer (NSCLC). The present study aimed to investigate the role of hsa_circ_0058357 on the progression of NSCLC. Cell proliferation, migration and apoptosis were determined using Cell Counting Kit-8, Transwell and flow cytometry assays, respectively. Gene [circRNA and microRNA (miR)] and protein expression levels were determined via reverse transcription-quantitative PCR and immunoblotting. A luciferase assay was employed to detect the binding of miR-24-3p with AVL9 cell migration associated (AVL9), while a cancer xenograft model was established to evaluate cancer growth in vivo. The results demonstrated that hsa_circ_0058357 was highly expressed in human NSCLC tissues and NSCLC cells compared with para-cancerous tissues and human bronchial epithelial (HBE) cells, respectively. Knockdown of hsa_circ_0058357 significantly suppressed cell viability, migration and tumor growth, while it promoted apoptosis in NSCLC cells. As a competing endogenous RNA, hsa_circ_0058357 knockdown contributed to the increase of miR-24-3p expression in NSCLC cells. Of note, overexpression of miR-24-3p markedly abolished the exogenous hsa_circ_0058357-induced excessive proliferation, migration and apoptosis resistance of NSCLC cells. Mechanistically, as a signaling molecule in late secretory pathway, AVL9 was also expressed at a high level in NSCLC tissues and cells, which could be directly suppressed by miR-24-3p. In the tumor tissues, along with growth inhibition, hsa_circ_0058357 knockdown also mediated the elevation of miR-24-3p and the reduction of AVL9. Thus, it was suggested that hsa_circ_0058357 may be a crucial regulation factor in NSCLC by sponging hsa-miR-24-3p, leading to a decrease in miR-24-3p expression, and subsequent increase in AVL9 expression. Therefore, hsa_circ_0058357 may serve as a potential target for diagnosis and gene therapy for NSCLC.
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Affiliation(s)
- Dongshan Wei
- Department of Cardiothoracic Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, P.R. China
| | - Lifang Sun
- Department of Tuberculosis, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, P.R. China
| | - Wei Feng
- Department of Cancer Diagnosis and Treatment, Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310000, P.R. China
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15
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Herstad KMV, Gunnes G, Rørtveit R, Kolbjørnsen Ø, Tran L, Skancke E. Immunohistochemical expression of β-catenin, Ki67, CD3 and CD18 in canine colorectal adenomas and adenocarcinomas. BMC Vet Res 2021; 17:119. [PMID: 33712002 PMCID: PMC7953700 DOI: 10.1186/s12917-021-02829-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 03/05/2021] [Indexed: 12/18/2022] Open
Abstract
Background Inflammation is believed to influence human colorectal carcinogenesis and may have an impact on prognosis and survival. The mucosal immunophenotype in dogs with colorectal cancer is poorly described. The aim of this study was to investigate whether the density, distribution and grade of tumor-infiltrating immune cells (TIIs) are different in normal colonic tissue vs benign stages (adenomas) and malignant stages (adenocarcinomas) of canine colorectal carcinogenesis, and thus, whether they can be considered as prognostic factors in dogs. This retrospective case-control study was performed on formalin-fixed, paraffin-embedded tissue samples from dogs with histologically confirmed colorectal adenoma (n = 18) and adenocarcinoma (n = 13) collected from archived samples. The samples had been collected by colonoscopy, surgery or during postmortem examination. Healthy colonic tissue obtained post mortem from dogs euthanized for reasons not involving the gastrointestinal tract served as control tissue (n = 9). Results The tumor samples had significantly lower numbers of CD3+ T-cells in the epithelium compared to controls (adenocarcinoma vs control, Kruskal-Wallis test, p = 0.0004, and adenoma vs control, p = 0.002). Adenomas had a significantly lower number of CD18+ cells in the lamina propria, compared to control samples (Kruskal-Wallis test, p = 0.008). Colonic samples from control dogs had uniform staining of β-catenin along the cell membrane of epithelial cells. Compared to normal colonic cells, the expression levels of cytoplasmic β-catenin were significantly higher in adenomas and adenocarcinomas (adenoma vs control Kruskal-Wallis test, p = 0.004, and adenocarcinoma vs control, p = 0.002). None of the control samples showed positive staining of β-catenin in the nucleus of colonic cells. In contrast, adenocarcinomas and adenomas showed moderate to strong staining of the cell nucleus. The nuclear β-catenin expression (signal strength and distribution) was significantly higher in adenomas compared to adenocarcinomas (Kruskal-Wallis test, p < 0.05). Conclusions β-catenin and Ki67 were not useful markers for demonstrating tumor progression from adenomas to adenocarcinomas. The lower presence of CD18 and CD3+ cells in colorectal tumors compared to controls indicates a reduced presence of histiocytes and T-cells, which may have implications for the pathogenesis and progression of colorectal cancer in dogs. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-021-02829-6.
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Affiliation(s)
- Kristin M V Herstad
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Oslo, Norway.
| | - Gjermund Gunnes
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Oslo, Norway
| | - Runa Rørtveit
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Oslo, Norway
| | - Øyvor Kolbjørnsen
- Department of Animal Health, Norwegian Veterinary Institute, Section for Biohazard and Pathology, Oslo, Norway
| | - Linh Tran
- Department of Animal Health, Norwegian Veterinary Institute, Section for Biohazard and Pathology, Oslo, Norway
| | - Ellen Skancke
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Oslo, Norway
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16
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Wang T, Kwon SH, Peng X, Urdy S, Lu Z, Schmitz RJ, Dalton S, Mostov KE, Zhao S. A Qualitative Change in the Transcriptome Occurs after the First Cell Cycle and Coincides with Lumen Establishment during MDCKII Cystogenesis. iScience 2020; 23:101629. [PMID: 33089114 PMCID: PMC7567049 DOI: 10.1016/j.isci.2020.101629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 08/05/2020] [Accepted: 09/25/2020] [Indexed: 01/12/2023] Open
Abstract
Madin-Darby canine kidney II (MDCKII) cells are widely used to study epithelial morphogenesis. To better understand this process, we performed time course RNA-seq analysis of MDCKII 3D cystogenesis, along with polarized 2D cells for comparison. Our study reveals a biphasic change in the transcriptome that occurs after the first cell cycle and coincides with lumen establishment. This change appears to be linked to translocation of β-catenin, supported by analyses with AVL9- and DENND5A-knockdown clones, and regulation by HNF1B, supported by ATAC-seq study. These findings indicate a qualitative change model for transcriptome remodeling during epithelial morphogenesis, leading to cell proliferation decrease and cell polarity establishment. Furthermore, our study reveals that active mitochondria are retained and chromatin accessibility decreases in 3D cysts but not in 2D polarized cells. This indicates that 3D culture is a better model than 2D culture for studying epithelial morphogenesis. The transcriptome switches after the first cell cycle and during MDCKII lumenogenesis The transcriptome switch is linked to β-catenin translocation and HNF1B activation Chromatin accessibility decreases during MDCKII cystogenesis Active mitochondria are maintained in 3D, but not 2D, epithelial morphogenesis
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Affiliation(s)
- Tianfang Wang
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Sang-Ho Kwon
- Department of Anatomy, University of California, San Francisco, CA 94143-2140, USA.,Department of Cellular Biology and Anatomy, Augusta University, Medical College of Georgia, 1460 Laney Walker Boulevard, CB2820A, Augusta, GA 30912, USA
| | - Xiao Peng
- Department of Anatomy, University of California, San Francisco, CA 94143-2140, USA
| | - Severine Urdy
- Department of Anatomy, University of California, San Francisco, CA 94143-2140, USA
| | - Zefu Lu
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Stephen Dalton
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Keith E Mostov
- Department of Anatomy, University of California, San Francisco, CA 94143-2140, USA
| | - Shaying Zhao
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
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17
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Li D, Li N, Zhang YF, Fu H, Feng M, Schneider D, Su L, Wu X, Zhou J, Mackay S, Kramer J, Duan Z, Yang H, Kolluri A, Hummer AM, Torres MB, Zhu H, Hall MD, Luo X, Chen J, Wang Q, Abate-Daga D, Dropulic B, Hewitt SM, Orentas RJ, Greten TF, Ho M. Persistent Polyfunctional Chimeric Antigen Receptor T Cells That Target Glypican 3 Eliminate Orthotopic Hepatocellular Carcinomas in Mice. Gastroenterology 2020; 158:2250-2265.e20. [PMID: 32060001 PMCID: PMC7282931 DOI: 10.1053/j.gastro.2020.02.011] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 01/31/2020] [Accepted: 02/03/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS Glypican 3 (GPC3) is an oncofetal antigen involved in Wnt-dependent cell proliferation that is highly expressed in hepatocellular carcinoma (HCC). We investigated whether the functions of chimeric antigen receptors (CARs) that target GPC3 are affected by their antibody-binding properties. METHODS We collected peripheral blood mononuclear cells from healthy donors and patients with HCC and used them to create CAR T cells, based on the humanized YP7 (hYP7) and HN3 antibodies, which have high affinities for the C-lobe and N-lobe of GPC3, respectively. NOD/SCID/IL-2Rgcnull (NSG) mice were given intraperitoneal injections of luciferase-expressing (Luc) Hep3B or HepG2 cells and after xenograft tumors formed, mice were given injections of saline or untransduced T cells (mock control), or CAR (HN3) T cells or CAR (hYP7) T cells. In other NOD/SCID/IL-2Rgcnull (NSG) mice, HepG2-Luc or Hep3B-Luc cells were injected into liver, and after orthotopic tumors formed, mice were given 1 injection of CAR (hYP7) T cells or CD19 CAR T cells (control). We developed droplet digital polymerase chain reaction and genome sequencing methods to analyze persistent CAR T cells in mice. RESULTS Injections of CAR (hYP7) T cells eliminated tumors in 66% of mice by week 3, whereas CAR (HN3) T cells did not reduce tumor burden. Mice given CAR (hYP7) T cells remained tumor free after re-challenge with additional Hep3B cells. The CAR T cells induced perforin- and granzyme-mediated apoptosis and reduced levels of active β-catenin in HCC cells. Mice injected with CAR (hYP7) T cells had persistent expansion of T cells and subsets of polyfunctional CAR T cells via antigen-induced selection. These T cells were observed in the tumor microenvironment and spleen for up to 7 weeks after CAR T-cell administration. Integration sites in pre-infusion CAR (HN3) and CAR (hYP7) T cells were randomly distributed, whereas integration into NUPL1 was detected in 3.9% of CAR (hYP7) T cells 5 weeks after injection into tumor-bearing mice and 18.1% of CAR (hYP7) T cells at week 7. There was no common site of integration in CAR (HN3) or CD19 CAR T cells from tumor-bearing mice. CONCLUSIONS In mice with xenograft or orthoptic liver tumors, CAR (hYP7) T cells eliminate GPC3-positive HCC cells, possibly by inducing perforin- and granzyme-mediated apoptosis or reducing Wnt signaling in tumor cells. GPC3-targeted CAR T cells might be developed for treatment of patients with HCC.
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MESH Headings
- Aged
- Aged, 80 and over
- Animals
- Apoptosis
- Carcinoma, Hepatocellular/immunology
- Carcinoma, Hepatocellular/metabolism
- Carcinoma, Hepatocellular/pathology
- Carcinoma, Hepatocellular/therapy
- Cell Proliferation
- Female
- Gene Expression Regulation, Neoplastic
- Glypicans/genetics
- Glypicans/immunology
- Glypicans/metabolism
- Granzymes/metabolism
- Hep G2 Cells
- Humans
- Immunotherapy, Adoptive
- Liver Neoplasms/immunology
- Liver Neoplasms/metabolism
- Liver Neoplasms/pathology
- Liver Neoplasms/therapy
- Male
- Mice, Inbred NOD
- Mice, SCID
- Middle Aged
- Perforin/metabolism
- Receptors, Chimeric Antigen/genetics
- Receptors, Chimeric Antigen/immunology
- Receptors, Chimeric Antigen/metabolism
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- T-Lymphocytes/transplantation
- Tumor Burden
- Tumor Microenvironment
- Wnt Signaling Pathway
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Dan Li
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland; School of Life Sciences, East China Normal University, Shanghai, China
| | - Nan Li
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Yi-Fan Zhang
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Haiying Fu
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland; Department of Immunology, Norman Bethune College of Medicine, Jilin University, Changchun, China
| | - Mingqian Feng
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Dina Schneider
- Lentingen, a Miltenyi Biotec Company, Gaithersburg, Maryland
| | - Ling Su
- Cancer Research Technology Program, Leidos Biomedical Research, Inc, Frederick, Maryland
| | - Xiaolin Wu
- Cancer Research Technology Program, Leidos Biomedical Research, Inc, Frederick, Maryland
| | - Jing Zhou
- IsoPlexis Corporation, Branford, Connecticut
| | - Sean Mackay
- IsoPlexis Corporation, Branford, Connecticut
| | - Josh Kramer
- Animal Facility, Leidos Biomedical Research, Inc, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Zhijian Duan
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Hongjia Yang
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Aarti Kolluri
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Alissa M Hummer
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Madeline B Torres
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Hu Zhu
- Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland
| | - Matthew D Hall
- Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland
| | - Xiaoling Luo
- Collaborative Protein Technology Resource, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Jinqiu Chen
- Collaborative Protein Technology Resource, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Qun Wang
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Daniel Abate-Daga
- Departments of Immunology, Cutaneous Oncology, and Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Boro Dropulic
- Lentingen, a Miltenyi Biotec Company, Gaithersburg, Maryland
| | - Stephen M Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | | | - Tim F Greten
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Mitchell Ho
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
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18
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Gao M, Kong W, Huang Z, Xie Z. Identification of Key Genes Related to Lung Squamous Cell Carcinoma Using Bioinformatics Analysis. Int J Mol Sci 2020; 21:ijms21082994. [PMID: 32340320 PMCID: PMC7215920 DOI: 10.3390/ijms21082994] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/10/2020] [Accepted: 04/21/2020] [Indexed: 01/30/2023] Open
Abstract
Lung squamous cell carcinoma (LUSC) is often diagnosed at the advanced stage with poor prognosis. The mechanisms of its pathogenesis and prognosis require urgent elucidation. This study was performed to screen potential biomarkers related to the occurrence, development and prognosis of LUSC to reveal unknown physiological and pathological processes. Using bioinformatics analysis, the lung squamous cell carcinoma microarray datasets from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases were analyzed to identify differentially expressed genes (DEGs). Furthermore, PPI and WGCNA network analysis were integrated to identify the key genes closely related to the process of LUSC development. In addition, survival analysis was performed to achieve a prognostic model that accomplished good prediction accuracy. Three hundred and thirty–seven up–regulated and 119 down-regulated genes were identified, in which four genes have been found to play vital roles in LUSC development, namely CCNA2, AURKA, AURKB, and FEN1. The prognostic model contained 5 genes, which were all detrimental to prognosis. The AUC of the established prognostic model for predicting the survival of patients at 1, 3, and 5 years was 0.692, 0.722, and 0.651 in the test data, respectively. In conclusion, this study identified several biomarkers of significant interest for additional investigation of the therapies and methods of prognosis of lung squamous cell carcinoma.
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Affiliation(s)
- Miaomiao Gao
- Peking University International Cancer Institute and Department of Pharmacology, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Weikaixin Kong
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zhuo Huang
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
- Correspondence: (Z.H.); (Z.X.)
| | - Zhengwei Xie
- Peking University International Cancer Institute and Department of Pharmacology, School of Basic Medical Sciences, Peking University, Beijing 100191, China
- Correspondence: (Z.H.); (Z.X.)
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19
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Wang J, Wang T, Sun Y, Feng Y, Kisseberth WC, Henry CJ, Mok I, Lana SE, Dobbin K, Northrup N, Howerth EW, Zhao S. Proliferative and Invasive Colorectal Tumors in Pet Dogs Provide Unique Insights into Human Colorectal Cancer. Cancers (Basel) 2018; 10:cancers10090330. [PMID: 30223484 PMCID: PMC6162437 DOI: 10.3390/cancers10090330] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 09/12/2018] [Accepted: 09/12/2018] [Indexed: 12/13/2022] Open
Abstract
Spontaneous tumors in pet dogs represent a valuable but undercharacterized cancer model. To better use this resource, we performed an initial global comparison between proliferative and invasive colorectal tumors from 20 canine cases, and evaluated their molecular homology to human colorectal cancer (CRC). First, proliferative canine tumors harbor overactivated WNT/β-catenin pathways and recurrent CTNNB1 (β-catenin) mutations S45F/P, D32Y and G34E. Invasive canine tumors harbor prominent fibroblast proliferation and overactivated stroma. Both groups have recurrent TP53 mutations. We observed three invasion patterns in canine tumors: collective, crypt-like and epithelial–mesenchymal transition (EMT). We detected enriched Helicobacter bilis and Alistipes finegoldii in proliferative and crypt-like tumors, but depleted mucosa-microbes in the EMT tumor. Second, guided by our canine findings, we classified 79% of 478 human colon cancers from The Cancer Genome Atlas into four subtypes: primarily proliferative, or with collective, crypt-like or EMT invasion features. Their molecular characteristics match those of canine tumors. We showed that consensus molecular subtype 4 (mesenchymal) of human CRC should be further divided into EMT and crypt-like subtypes, which differ in TGF-β activation and mucosa-microbe content. Our canine tumors share the same pathogenic pathway as human CRCs. Dog-human integration identifies three CRC invasion patterns and improves CRC subtyping.
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Affiliation(s)
- Jin Wang
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
| | - Tianfang Wang
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
| | - Yanfang Sun
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
| | - Yuan Feng
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
| | - William C Kisseberth
- Department of Veterinary Clinical Sciences, the Ohio State University College of Veterinary Medicine, Columbus, OH 43210, USA.
| | - Carolyn J Henry
- College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA.
| | - Irene Mok
- Flint Animal Cancer Center, Colorado State University, Fort Collins, CO 80525, USA.
| | - Susan E Lana
- Flint Animal Cancer Center, Colorado State University, Fort Collins, CO 80525, USA.
| | - Kevin Dobbin
- Department of Biostatistics, University of Georgia, Athens, GA 30602, USA.
| | - Nicole Northrup
- College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
| | - Elizabeth W Howerth
- College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
| | - Shaying Zhao
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
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20
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Zhang M, Liu D, Tang J, Feng Y, Wang T, Dobbin KK, Schliekelman P, Zhao S. SEG - A Software Program for Finding Somatic Copy Number Alterations in Whole Genome Sequencing Data of Cancer. Comput Struct Biotechnol J 2018; 16:335-341. [PMID: 30258547 PMCID: PMC6154469 DOI: 10.1016/j.csbj.2018.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/31/2018] [Accepted: 09/01/2018] [Indexed: 01/15/2023] Open
Abstract
As next-generation sequencing technology advances and the cost decreases, whole genome sequencing (WGS) has become the preferred platform for the identification of somatic copy number alteration (CNA) events in cancer genomes. To more effectively decipher these massive sequencing data, we developed a software program named SEG, shortened from the word “segment”. SEG utilizes mapped read or fragment density for CNA discovery. To reduce CNA artifacts arisen from sequencing and mapping biases, SEG first normalizes the data by taking the log2-ratio of each tumor density against its matching normal density. SEG then uses dynamic programming to find change-points among a contiguous log2-ratio data series along a chromosome, dividing the chromosome into different segments. SEG finally identifies those segments having CNA. Our analyses with both simulated and real sequencing data indicate that SEG finds more small CNAs than other published software tools.
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Affiliation(s)
- Mucheng Zhang
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA30602-7229, USA
| | - Deli Liu
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA30602-7229, USA
| | - Jie Tang
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA30602-7229, USA
| | - Yuan Feng
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA30602-7229, USA
| | - Tianfang Wang
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA30602-7229, USA
| | - Kevin K Dobbin
- Department of Biostatistics, University of Georgia, Athens, GA30602-7229, USA
| | - Paul Schliekelman
- Department of Statistics, University of Georgia, Athens, GA30602-7229, USA
| | - Shaying Zhao
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA30602-7229, USA
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21
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Hendricks WPD, Zismann V, Sivaprakasam K, Legendre C, Poorman K, Tembe W, Perdigones N, Kiefer J, Liang W, DeLuca V, Stark M, Ruhe A, Froman R, Duesbery NS, Washington M, Aldrich J, Neff MW, Huentelman MJ, Hayward N, Brown K, Thamm D, Post G, Khanna C, Davis B, Breen M, Sekulic A, Trent JM. Somatic inactivating PTPRJ mutations and dysregulated pathways identified in canine malignant melanoma by integrated comparative genomic analysis. PLoS Genet 2018; 14:e1007589. [PMID: 30188888 PMCID: PMC6126841 DOI: 10.1371/journal.pgen.1007589] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/24/2018] [Indexed: 01/11/2023] Open
Abstract
Canine malignant melanoma, a significant cause of mortality in domestic dogs, is a powerful comparative model for human melanoma, but little is known about its genetic etiology. We mapped the genomic landscape of canine melanoma through multi-platform analysis of 37 tumors (31 mucosal, 3 acral, 2 cutaneous, and 1 uveal) and 17 matching constitutional samples including long- and short-insert whole genome sequencing, RNA sequencing, array comparative genomic hybridization, single nucleotide polymorphism array, and targeted Sanger sequencing analyses. We identified novel predominantly truncating mutations in the putative tumor suppressor gene PTPRJ in 19% of cases. No BRAF mutations were detected, but activating RAS mutations (24% of cases) occurred in conserved hotspots in all cutaneous and acral and 13% of mucosal subtypes. MDM2 amplifications (24%) and TP53 mutations (19%) were mutually exclusive. Additional low-frequency recurrent alterations were observed amidst low point mutation rates, an absence of ultraviolet light mutational signatures, and an abundance of copy number and structural alterations. Mutations that modulate cell proliferation and cell cycle control were common and highlight therapeutic axes such as MEK and MDM2 inhibition. This mutational landscape resembles that seen in BRAF wild-type and sun-shielded human melanoma subtypes. Overall, these data inform biological comparisons between canine and human melanoma while suggesting actionable targets in both species.
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Affiliation(s)
- William P. D. Hendricks
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Victoria Zismann
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Karthigayini Sivaprakasam
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
- Department of Biomedical Informatics, Arizona State University, Phoenix, Arizona, United States of America
| | - Christophe Legendre
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Kelsey Poorman
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States of America
- Department of Dermatology, Mayo Clinic, Scottsdale, Arizona, United States of America
| | - Waibhav Tembe
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Nieves Perdigones
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Jeffrey Kiefer
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Winnie Liang
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Valerie DeLuca
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
- School of Life Sciences, Arizona State University, Phoenix, Arizona, United States of America
| | - Mitchell Stark
- Dermatology Research Centre, The University of Queensland, The University of Queensland Diamantina Institute, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Alison Ruhe
- Veterinary Genetics Laboratory, University of California Davis, Davis, California, United States of America
| | - Roe Froman
- Laboratory of Cancer and Developmental Cell Biology, Van Andel Research Institute (VARI), Grand Rapids, Michigan, United States of America
| | | | - Megan Washington
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Jessica Aldrich
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Mark W. Neff
- Program in Canine Genetics and Genomics, Van Andel Research Institute (VARI), Grand Rapids, Michigan, United States of America
| | - Matthew J. Huentelman
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Nicholas Hayward
- Oncogenomics Laboratory, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Kevin Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Douglas Thamm
- Flint Animal Cancer Center, Colorado State University, Fort Collins, Colorado, United States of America
| | - Gerald Post
- The Veterinary Cancer Center, Norwalk, Connecticut, United States of America
| | - Chand Khanna
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Barbara Davis
- Innogenics Inc., Harvard, Massachusetts, United States of America
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States of America
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States of America
| | - Alexander Sekulic
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
- Department of Dermatology, Mayo Clinic, Scottsdale, Arizona, United States of America
| | - Jeffrey M. Trent
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
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22
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Collaborating genomic, transcriptomic and microbiomic alterations lead to canine extreme intestinal polyposis. Oncotarget 2018; 9:29162-29179. [PMID: 30018743 PMCID: PMC6044369 DOI: 10.18632/oncotarget.25646] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/01/2018] [Indexed: 12/13/2022] Open
Abstract
Extreme intestinal polyposis in pet dogs has not yet been reported in literature. We identified a dog patient who developed numerous intestinal polyps, with the severity resembling human classic familial adenomatous polyposis (FAP), except the jejunum-ileum junction being the most polyp-dense. We investigated this dog, in comparison with 22 other dogs with spontaneous intestinal tumors but no severe polyposis, and with numerous published human cancers. We found, not APC mutation, but three other alteration pathways as likely reasons of this canine extreme polyposis. First, somatic truncation mutation W411X of FBXW7, a component of an E3 ubiquitin ligase, over-activates MYC and cell cycle-promoting network, accelerating crypt cell proliferation. Second, genes of protein trafficking and localization are downregulated, likely associated with germline mutation G406D of STAMBPL1, a K63-deubiquitinase, and MYC network activation. This inhibits epithelial apical-basolateral polarity establishment, preventing crypt cell differentiation. Third, Bacteroides uniformis, a commensal gut anaerobe, thrives and expresses abundantly thioredoxin and nitroreductase. These bacterial products could reduce oxidative stress linked to host germline mutation R51X of CYB5RL, a cytochrome b5 reductase homologue, decreasing cell death. Our work emphasizes the close collaboration of alterations across the genome, transcriptome and microbiome in promoting tumorigenesis.
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23
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Chen L, Dong Y, Wang X, Hao G, Huang Y, Gutin B, Zhu H. Epigenome-Wide Association Study of Dietary Fiber Intake in African American Adolescents. Mol Nutr Food Res 2018; 62:e1800155. [PMID: 29644791 DOI: 10.1002/mnfr.201800155] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 03/26/2018] [Indexed: 12/17/2022]
Abstract
SCOPE Low fiber intake is associated with increased risk for cardiovascular disease (CVD) and cancer. However, the underlying mechanisms are not well understood. Two hypotheses are tested: 1) dietary fiber would be associated with DNA methylation levels; 2) those DNA methylation changes would be associated with visceral adiposity and inflammation. Also the possibility that the associations between fiber and DNA methylation levels might be confounded with folic acid intake as sensitivity analysis are explored. METHODS AND RESULTS An epigenome-wide association study is conducted using Illumina 450K Bead-Chip on leukocyte DNA in 284 African American adolescents. Linear regression is performed to identify differentially methylated CpG sites associated with fiber. The methylation levels of 3 CpG sites (cg15200711, cg19462022, and cg07035602) in LPCAT1 and RASA3 genes are associated with fiber (false discovery rate [FDR] < 0.05) after adjustment for covariates including folic acid. The methylation levels of cg07035602 and cg19462022 are also associated with visceral adiposity and inflammation. CONCLUSIONS The data show that DNA methylation levels at LPCAT1 and RASA3 genes are associated with dietary fiber intake as well as with adiposity and inflammation. Future studies are warranted to determine whether epigenetic regulation may underlie the beneficial effects of fiber intake on adiposity and inflammation.
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Affiliation(s)
- Li Chen
- Georgia Prevention Institute, Department of Population Health Sciences, Medical College of Georgia, Augusta University, 1120 15th Street, HS-1640, Augusta, Georgia, USA
| | - Yanbin Dong
- Georgia Prevention Institute, Department of Population Health Sciences, Medical College of Georgia, Augusta University, 1120 15th Street, HS-1640, Augusta, Georgia, USA
| | - Xiaoling Wang
- Georgia Prevention Institute, Department of Population Health Sciences, Medical College of Georgia, Augusta University, 1120 15th Street, HS-1640, Augusta, Georgia, USA
| | - Guang Hao
- Georgia Prevention Institute, Department of Population Health Sciences, Medical College of Georgia, Augusta University, 1120 15th Street, HS-1640, Augusta, Georgia, USA
| | - Ying Huang
- Georgia Prevention Institute, Department of Population Health Sciences, Medical College of Georgia, Augusta University, 1120 15th Street, HS-1640, Augusta, Georgia, USA
| | - Bernard Gutin
- Georgia Prevention Institute, Department of Population Health Sciences, Medical College of Georgia, Augusta University, 1120 15th Street, HS-1640, Augusta, Georgia, USA
| | - Haidong Zhu
- Georgia Prevention Institute, Department of Population Health Sciences, Medical College of Georgia, Augusta University, 1120 15th Street, HS-1640, Augusta, Georgia, USA
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24
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Lin H, Fan X, He L, Zhou D. Methylation patterns of RASA3 associated with clinicopathological factors in hepatocellular carcinoma. J Cancer 2018; 9:2116-2122. [PMID: 29937930 PMCID: PMC6010675 DOI: 10.7150/jca.24567] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 03/31/2018] [Indexed: 12/25/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the sixth most common tumor worldwide. The relationship between the gene methylation accumulation and HCC has been widely studied. In our study, we used the Sequenom EpiTYPER assay to investigate the methylation levels of the RASA3 in 164 HCC samples and paired adjacent non-cancerous tissues, and the association between methylation level and clinicopathological features. The methylation level of the RASA3 in HCC samples was found significantly lower than that in the adjacent non-cancerous tissues (P<0.0001). Moreover, the hypomethylation of RASA3 in HCC samples was connected with the presence of tumornecrosis (P=0.029) and alcohol intake (P=0.002). Furthermore, it was found that the expression of RASA3 was significantly decreased in tumor tissues (P=0.0053), which was also correlated with the methylation levels of RASA3 gene. Thus, RASA3 hypomethylation is a common feature in HCC, and may be a potential mechanism for HCC development, and serves as a useful biomarker for the early detection, especially in alcohol-associated HCCs.
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Affiliation(s)
- Hui Lin
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Biomedical Research Center, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaoxiao Fan
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Biomedical Research Center, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - LiFeng He
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Biomedical Research Center, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Daizhan Zhou
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Biomedical Research Center, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Bio-X Center, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China.,Present address: Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine; Institute of Medical Genetics, Tongji University, Shanghai, China
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25
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Herstad KMV, Rønning HT, Bakke AM, Moe L, Skancke E. Changes in the faecal bile acid profile in dogs fed dry food vs high content of beef: a pilot study. Acta Vet Scand 2018; 60:29. [PMID: 29751815 PMCID: PMC5948804 DOI: 10.1186/s13028-018-0383-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 05/03/2018] [Indexed: 12/31/2022] Open
Abstract
Background Dogs are fed various diets, which also include components of animal origin. In humans, a high-fat/low-fibre diet is associated with higher faecal levels of bile acids, which can influence intestinal health. It is unknown how an animal-based diet high in fat and low in fibre influences the faecal bile acid levels and intestinal health in dogs. This study investigated the effects of high intake of minced beef on the faecal bile acid profile in healthy, adult, client-owned dogs (n = 8) in a 7-week trial. Dogs were initially adapted to the same commercial dry food. Thereafter, incremental substitution of the dry food by boiled minced beef over 3 weeks resulted in a diet in which 75% of each dog’s total energy requirement was provided as minced beef during week 5. Dogs were subsequently reintroduced to the dry food for the last 2 weeks of the study. The total taurine and glycine-conjugated bile acids, the primary bile acids chenodeoxycholic acid and cholic acid, and the secondary bile acids lithocholic acid, deoxycholic acid (DCA) and ursodeoxycholic acid (UDCA) were analysed, using liquid chromatography–tandem mass spectrometry. Results The faecal quantities of DCA were significantly higher in dogs fed the high minced beef diet. These levels reversed when dogs were reintroduced to the dry food diet. The faecal levels of UDCA and taurine-conjugated bile acids had also increased in response to the beef diet, but this was only significant when compared to the last dry food period. Conclusions These results suggest that an animal-based diet with high-fat/low-fibre content can influence the faecal bile acids levels. The consequences of this for canine colonic health will require further investigation. Electronic supplementary material The online version of this article (10.1186/s13028-018-0383-7) contains supplementary material, which is available to authorized users.
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26
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Mochel JP, Jergens AE, Kingsbury D, Kim HJ, Martín MG, Allenspach K. Intestinal Stem Cells to Advance Drug Development, Precision, and Regenerative Medicine: A Paradigm Shift in Translational Research. AAPS JOURNAL 2017; 20:17. [PMID: 29234895 PMCID: PMC6044282 DOI: 10.1208/s12248-017-0178-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/21/2017] [Indexed: 12/23/2022]
Abstract
Recent advances in our understanding of the intestinal stem cell niche and the role of key signaling pathways on cell growth and maintenance have allowed the development of fully differentiated epithelial cells in 3D organoids. Stem cell-derived organoids carry significant levels of proteins that are natively expressed in the gut and have important roles in drug transport and metabolism. They are, therefore, particularly relevant to study the gastrointestinal (GI) absorption of oral medications. In addition, organoids have the potential to serve as a robust preclinical model for demonstrating the effectiveness of new drugs more rapidly, with more certainty, and at lower costs compared with live animal studies. Importantly, because they are derived from individuals with different genotypes, environmental risk factors and drug sensitivity profiles, organoids are a highly relevant screening system for personalized therapy in both human and veterinary medicine. Lastly, and in the context of patient-specific congenital diseases, orthotopic transplantation of engineered organoids could repair and/or replace damaged epithelial tissues reported in various GI diseases, such as inflammatory bowel disease, cystic fibrosis, and tuft enteropathy. Ongoing translational research on organoids derived from dogs with naturally occurring digestive disorders has the potential to improve the predictability of preclinical models used for optimizing the therapeutic management of severe chronic enteropathies in human patients.
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Affiliation(s)
- Jonathan P Mochel
- Department of Biomedical Sciences, Iowa State University College of Veterinary Medicine, 2448 Lloyd, 1809 S Riverside Dr., Ames, Iowa, 50011-1250, USA.
| | - Albert E Jergens
- Department of Veterinary Clinical Sciences, Iowa State University College of Veterinary Medicine, 50011-1250 Ames, Iowa, USA
| | - Dawn Kingsbury
- Department of Veterinary Clinical Sciences, Iowa State University College of Veterinary Medicine, 50011-1250 Ames, Iowa, USA
| | - Hyun Jung Kim
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, 78712, USA
| | - Martín G Martín
- Department of Pediatrics, University of California Los Angeles, California, Los Angeles, 90095-1782, USA
| | - Karin Allenspach
- Department of Veterinary Clinical Sciences, Iowa State University College of Veterinary Medicine, 50011-1250 Ames, Iowa, USA
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27
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Baldassarri M, Fallerini C, Cetta F, Ghisalberti M, Bellan C, Furini S, Spiga O, Crispino S, Gotti G, Ariani F, Paladini P, Renieri A, Frullanti E. Omic Approach in Non-smoker Female with Lung Squamous Cell Carcinoma Pinpoints to Germline Susceptibility and Personalized Medicine. Cancer Res Treat 2017; 50:356-365. [PMID: 28546520 PMCID: PMC5912139 DOI: 10.4143/crt.2017.125] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 04/25/2017] [Indexed: 12/11/2022] Open
Abstract
Purpose Lung cancer is strongly associated to tobacco smoking. However, global statistics estimate that in females the proportion of lung cancer cases that is unrelated to tobacco smoking reaches fifty percent, making questionable the etiology of the disease. Materials and Methods A never-smoker female with primary EGFR/KRAS/ALK-negative squamous cell carcinoma of the lung and their normal sibswere subjected to a novel integrative “omic” approach using a pedigree-based model for discovering genetic factors leading to cancer in the absence of well-known environmental trigger. A first-stepwhole-exome sequencing on tumor and normal tissue did not identify mutations in known driver genes. Building on the idea of a germline oligogenic origin of lung cancer, we performed whole-exome sequencing of DNA from patients’ peripheral blood and their unaffected sibs. Finally, RNA-sequencing analysis in tumoral and matched non-tumoral tissues was carried out in order to investigate the clonal profile and the pathogenic role of the identified variants. Results Filtering for rare variants with Combined Annotation Dependent Depletion (CADD) > 25 and potentially damaging effect, we identified rare/private germline deleterious variants in 11 cancer-associated genes, none ofwhich, except one, sharedwith the healthy sib, pinpointing to a “private” oligogenic germline signature. Noteworthy, among these, two mutated genes, namely ACACA and DEPTOR, turned to be potential targets for therapy because related to known drivers, such as BRCA1 and EGFR. Conclusion In the era of precision medicine, this report emphasizes the importance of an “omic” approach to uncover oligogenic germline signature underlying cancer development and to identify suitable therapeutic targets as well.
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Affiliation(s)
- Margherita Baldassarri
- Medical Genetics Unit, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | | | | | - Marco Ghisalberti
- Thoracic Surgery Unit, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Cristiana Bellan
- Section of Pathology, Department of Medical Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Simone Furini
- Department of Medical Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Ottavia Spiga
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Sergio Crispino
- Medical Oncology Unit, Azienda Usl Toscana Sudest, Siena, Italy
| | - Giuseppe Gotti
- Thoracic Surgery Unit, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Francesca Ariani
- Medical Genetics Unit, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Piero Paladini
- Thoracic Surgery Unit, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Alessandra Renieri
- Medical Genetics Unit, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
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28
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Qamra A, Xing M, Padmanabhan N, Kwok JJT, Zhang S, Xu C, Leong YS, Lee Lim AP, Tang Q, Ooi WF, Suling Lin J, Nandi T, Yao X, Ong X, Lee M, Tay ST, Keng ATL, Gondo Santoso E, Ng CCY, Ng A, Jusakul A, Smoot D, Ashktorab H, Rha SY, Yeoh KG, Peng Yong W, Chow PK, Chan WH, Ong HS, Soo KC, Kim KM, Wong WK, Rozen SG, Teh BT, Kappei D, Lee J, Connolly J, Tan P. Epigenomic Promoter Alterations Amplify Gene Isoform and Immunogenic Diversity in Gastric Adenocarcinoma. Cancer Discov 2017; 7:630-651. [DOI: 10.1158/2159-8290.cd-16-1022] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 10/27/2016] [Accepted: 03/16/2017] [Indexed: 01/08/2023]
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Graham NA, Minasyan A, Lomova A, Cass A, Balanis NG, Friedman M, Chan S, Zhao S, Delgado A, Go J, Beck L, Hurtz C, Ng C, Qiao R, Ten Hoeve J, Palaskas N, Wu H, Müschen M, Multani AS, Port E, Larson SM, Schultz N, Braas D, Christofk HR, Mellinghoff IK, Graeber TG. Recurrent patterns of DNA copy number alterations in tumors reflect metabolic selection pressures. Mol Syst Biol 2017; 13:914. [PMID: 28202506 PMCID: PMC5327725 DOI: 10.15252/msb.20167159] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 01/12/2017] [Accepted: 01/16/2017] [Indexed: 12/28/2022] Open
Abstract
Copy number alteration (CNA) profiling of human tumors has revealed recurrent patterns of DNA amplifications and deletions across diverse cancer types. These patterns are suggestive of conserved selection pressures during tumor evolution but cannot be fully explained by known oncogenes and tumor suppressor genes. Using a pan-cancer analysis of CNA data from patient tumors and experimental systems, here we show that principal component analysis-defined CNA signatures are predictive of glycolytic phenotypes, including 18F-fluorodeoxy-glucose (FDG) avidity of patient tumors, and increased proliferation. The primary CNA signature is enriched for p53 mutations and is associated with glycolysis through coordinate amplification of glycolytic genes and other cancer-linked metabolic enzymes. A pan-cancer and cross-species comparison of CNAs highlighted 26 consistently altered DNA regions, containing 11 enzymes in the glycolysis pathway in addition to known cancer-driving genes. Furthermore, exogenous expression of hexokinase and enolase enzymes in an experimental immortalization system altered the subsequent copy number status of the corresponding endogenous loci, supporting the hypothesis that these metabolic genes act as drivers within the conserved CNA amplification regions. Taken together, these results demonstrate that metabolic stress acts as a selective pressure underlying the recurrent CNAs observed in human tumors, and further cast genomic instability as an enabling event in tumorigenesis and metabolic evolution.
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Affiliation(s)
- Nicholas A Graham
- Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Molecular & Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, USA
| | - Aspram Minasyan
- Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Molecular & Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Anastasia Lomova
- Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Molecular & Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Ashley Cass
- Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Molecular & Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Nikolas G Balanis
- Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Molecular & Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Michael Friedman
- Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Molecular & Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Shawna Chan
- Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Molecular & Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Sophie Zhao
- Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Molecular & Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Adrian Delgado
- Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Molecular & Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - James Go
- Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Molecular & Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Lillie Beck
- Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Molecular & Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Christian Hurtz
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Carina Ng
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Rong Qiao
- Department of Molecular & Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Johanna Ten Hoeve
- Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Molecular & Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Nicolaos Palaskas
- Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Molecular & Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Hong Wu
- Department of Molecular & Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- School of Life Sciences & Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Markus Müschen
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Asha S Multani
- Department of Genetics, M. D. Anderson Cancer Center, The University of Texas, Houston, TX, USA
| | - Elisa Port
- Department of Surgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven M Larson
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Braas
- Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Molecular & Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- UCLA Metabolomics Center, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Heather R Christofk
- Department of Molecular & Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- UCLA Metabolomics Center, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Ingo K Mellinghoff
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medical College, New York, NY, USA
- Department of Neurology, Weill Cornell Medical College, New York, NY, USA
| | - Thomas G Graeber
- Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Molecular & Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- UCLA Metabolomics Center, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- California NanoSystems Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
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Liu D, Xiong H, Ellis AE, Northrup NC, Dobbin KK, Shin DM, Zhao S. Canine spontaneous head and neck squamous cell carcinomas represent their human counterparts at the molecular level. PLoS Genet 2015; 11:e1005277. [PMID: 26030765 PMCID: PMC4452692 DOI: 10.1371/journal.pgen.1005277] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 05/14/2015] [Indexed: 01/15/2023] Open
Abstract
Spontaneous canine head and neck squamous cell carcinoma (HNSCC) represents an excellent model of human HNSCC but is greatly understudied. To better understand and utilize this valuable resource, we performed a pilot study that represents its first genome-wide characterization by investigating 12 canine HNSCC cases, of which 9 are oral, via high density array comparative genomic hybridization and RNA-seq. The analyses reveal that these canine cancers recapitulate many molecular features of human HNSCC. These include analogous genomic copy number abnormality landscapes and sequence mutation patterns, recurrent alteration of known HNSCC genes and pathways (e.g., cell cycle, PI3K/AKT signaling), and comparably extensive heterogeneity. Amplification or overexpression of protein kinase genes, matrix metalloproteinase genes, and epithelial-mesenchymal transition genes TWIST1 and SNAI1 are also prominent in these canine tumors. This pilot study, along with a rapidly growing body of literature on canine cancer, reemphasizes the potential value of spontaneous canine cancers in HNSCC basic and translational research.
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Affiliation(s)
- Deli Liu
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Huan Xiong
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Angela E. Ellis
- College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Nicole C. Northrup
- College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Kevin K. Dobbin
- Department of Biostatistics, University of Georgia, Athens, Georgia, United States of America
| | - Dong M. Shin
- Winship Cancer Center, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Shaying Zhao
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
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Li Y, Xu J, Xiong H, Ma Z, Wang Z, Kipreos ET, Dalton S, Zhao S. Cancer driver candidate genes AVL9, DENND5A and NUPL1 contribute to MDCK cystogenesis. Oncoscience 2014; 1:854-865. [PMID: 25621300 PMCID: PMC4303893 DOI: 10.18632/oncoscience.107] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 12/14/2014] [Indexed: 12/12/2022] Open
Abstract
AVL9, DENND5A and NUPL1 are among the cancer driver candidate genes previously identified via dog-human comparison, and may function in epithelial cell polarity as indicated by bioinformatics analysis. To better understand their cellular functions and roles in cancer, we knocked down each gene in MDCKII cells through shRNA and performed three-dimensional culture. Compared to the control, the knockdown clones developed significantly more abnormal cysts, e.g., cysts with the lumen harboring dead and/or live cells, or cysts having multiple lumens. Further analysis revealed that abnormalities initiated at the first cell division and persisted throughout the entire cystogenesis process. For NUPL1-knockdown cells, abnormal cytogenesis largely arose from faulty cell divisions, notably monopolar spindles or spindles with poorly separated poles. For AVL9- or DENND5A-knockdown cells, abnormalities originated from both aberrant intracellular trafficking and defective mitosis. Moreover, while all knockdown clones displayed an accelerated rate of both cell proliferation and death, only AVL9- and DENND5A-knockdowns, but not NUPL1-knockdown, promoted cell migration. These observations indicate that NUPL1 contributes to bipolar spindle formation, whereas AVL9 and DENND5A participate in both intracellular trafficking and cell cycle progression. Our study shed lights on these genes' normal cellular functions and on how their alteration contributes to carcinogenesis.
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Affiliation(s)
- Yaping Li
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens
| | - Jianing Xu
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens.,Current Address: Human Oncology & Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York
| | - Huan Xiong
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens
| | - Zhongyao Ma
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens
| | - Zhenghe Wang
- Department of Genetics & Genome Sciences and Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio
| | | | - Stephen Dalton
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens
| | - Shaying Zhao
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens
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Schurmans S, Polizzi S, Scoumanne A, Sayyed S, Molina-Ortiz P. The Ras/Rap GTPase activating protein RASA3: from gene structure to in vivo functions. Adv Biol Regul 2014; 57:153-61. [PMID: 25294679 DOI: 10.1016/j.jbior.2014.09.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 09/01/2014] [Accepted: 09/02/2014] [Indexed: 01/28/2023]
Abstract
RASA3 (or GTPase Activating Protein III, R-Ras GTPase-activating protein, GAP1(IP4BP)) is a GTPase activating protein of the GAP1 subfamily which targets Ras and Rap1. RASA3 was originally purified from pig platelet membranes through its intrinsic ability to bind inositol 1,3,4,5-tetrakisphosphate (I(1,3,4,5)P4) with high affinity, hence its first name GAP1(IP4BP) (for GAP1 subfamily member which binds I(1,3,4,5)P4). RASA3 was thus the first I(1,3,4,5)P4 receptor identified and cloned. The in vitro and in vivo functions of RASA3 remained somewhat elusive for a long time. However, recently, using genetically-modified mice and cells derived from these mice, the function of RASA3 during megakaryopoiesis, megakaryocyte adhesion and migration as well as integrin signaling has been reported. The goal of this review is thus to summarize and comment recent and less recent data in the literature on RASA3, in particular on the in vivo function of this specific GAP1 subfamily member.
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Affiliation(s)
- Stéphane Schurmans
- Laboratoire de Génétique Fonctionnelle, GIGA-Signal Transduction, GIGA B34, Université de Liège, Avenue de l'Hôpital 1, B-4000 Liège, Belgium; Secteur de Biochimie Métabolique, Département des Sciences Fonctionnelles, Faculté de Médecine Vétérinaire, Université de Liège, Boulevard de Colonster 20, 4000 Liège, Belgium; Welbio, Belgium.
| | - Séléna Polizzi
- Institut de Recherches Interdisciplinaires en Biologie Humaine et Moléculaire (IRIBHM), Institut de Biologie et de Médecine Moléculaires (IBMM), Faculté de Médecine, Université Libre de Bruxelles, Rue des Professeurs Jeener et Brachet 12, 6041 Gosselies, Belgium.
| | - Ariane Scoumanne
- Laboratoire de Génétique Fonctionnelle, GIGA-Signal Transduction, GIGA B34, Université de Liège, Avenue de l'Hôpital 1, B-4000 Liège, Belgium; Welbio, Belgium
| | - Sufyan Sayyed
- Laboratoire de Génétique Fonctionnelle, GIGA-Signal Transduction, GIGA B34, Université de Liège, Avenue de l'Hôpital 1, B-4000 Liège, Belgium
| | - Patricia Molina-Ortiz
- Laboratoire de Génétique Fonctionnelle, GIGA-Signal Transduction, GIGA B34, Université de Liège, Avenue de l'Hôpital 1, B-4000 Liège, Belgium; Welbio, Belgium
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Liu D, Xiong H, Ellis AE, Northrup NC, Rodriguez CO, O'Regan RM, Dalton S, Zhao S. Molecular homology and difference between spontaneous canine mammary cancer and human breast cancer. Cancer Res 2014; 74:5045-56. [PMID: 25082814 DOI: 10.1158/0008-5472.can-14-0392] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Spontaneously occurring canine mammary cancer represents an excellent model of human breast cancer, but is greatly understudied. To better use this valuable resource, we performed whole-genome sequencing, whole-exome sequencing, RNA-seq, and/or high-density arrays on twelve canine mammary cancer cases, including seven simple carcinomas and four complex carcinomas. Canine simple carcinomas, which histologically match human breast carcinomas, harbor extensive genomic aberrations, many of which faithfully recapitulate key features of human breast cancer. Canine complex carcinomas, which are characterized by proliferation of both luminal and myoepithelial cells and are rare in human breast cancer, seem to lack genomic abnormalities. Instead, these tumors have about 35 chromatin-modification genes downregulated and are abnormally enriched with active histone modification H4-acetylation, whereas aberrantly depleted with repressive histone modification H3K9me3. Our findings indicate the likelihood that canine simple carcinomas arise from genomic aberrations, whereas complex carcinomas originate from epigenomic alterations, reinforcing their unique value. Canine complex carcinomas offer an ideal system to study myoepithelial cells, the second major cell lineage of the mammary gland. Canine simple carcinomas, which faithfully represent human breast carcinomas at the molecular level, provide indispensable models for basic and translational breast cancer research.
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Affiliation(s)
- Deli Liu
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, Georgia
| | - Huan Xiong
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, Georgia
| | - Angela E Ellis
- College of Veterinary Medicine, University of Georgia, Athens, Georgia
| | - Nicole C Northrup
- College of Veterinary Medicine, University of Georgia, Athens, Georgia
| | - Carlos O Rodriguez
- School of Veterinary Medicine, University of California, Davis, California
| | - Ruth M O'Regan
- The Winship Cancer Center, Emory School of Medicine, Atlanta, Georgia
| | - Stephen Dalton
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, Georgia
| | - Shaying Zhao
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, Georgia.
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